some help required regarding my ngs data.
Description of the problem:
when I received some reads from illumina, first what i did is a quality check. This turned out to be terrible. Given 150-mers had a quality above 20 only in the first 80 positions. For everything else the quality dropped significantly. So then I started trimming these reads using bbduk (great tool never failed me before) and as a result I got that only 10% of reads passed the trimming process. I repeated the same process using trimmomatic and trimgalore and results were roughly the same. After googling for a while and reading illumina manuals i concluded that this is due to either high adaptor contamination associated with dimer sequencing or very short insert size. In all of the above cases I used the default adaptor list as provided by the above tools. Then I checked the lib prep manual to see if the stated adapters were in those default lists. The first one was, this was TruSeq_Universal_Adapter, however the second one was not. I never messed with adapters since there was never any need for me to do so (plus I haven't done a lot of mapping). However, the second one was very simmilar to TruSeq_Adapter_Index_23 (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATATCTCGTATGCCGTCTTCTGCTTG) but it had one insertion one deletion and one mutation : GATCGGAAGAGCACACGTCTGAACTCCAGTCACGaGTA-GtATCTCGTATGCCGTCTTCTGCTTG.
When I looked into my sequences a bit further I noticed that my fastq sequences started with PhiX_read2_adapter and another one which is not on the list. Totally confused at this point I decided to turn to you for help.
I have two index oligonucleotides .
Can anyone shed some light on this case. I received this data with very little info on it and was assigned a task to try to map it . I suspect there was some mixup with adapters but this is purely my inexperienced hunch. And if this is the likely case how do I go about creating a set of adapters myself? Also would you recommend trimming extra 15-20 NT from both ends so that better quality reads are obtained?
thank you so much